Methods for improved DNA release from binding substrates and/or decreasing PCR inhibition in pathogen detection

ABSTRACT

Disclosed herein are processes for collecting nucleic acids from particulate samples. One embodiment disclosed herein relates to the use of ultrasonic energy to simultaneously shear large nucleic acid molecules and large particulates to very small sizes prior to or during a chemical binding step to a nucleic acid binding surface. Another embodiment involves crushing the nucleic acid binding surface prior to eluting the bound nucleic acid molecules to enable better wetting of the nucleic acid binding surface and easier diffusion of bound nucleic acid molecules out of the nucleic acid binding surface.

CROSS-REFERENCE TO RELATED APPLICATION

This application claims benefit of U.S. Provisional Patent ApplicationNo. 61/452,786, filed Mar. 15, 2011, which is incorporated by referenceherein in its entirety.

FIELD OF INVENTION

The field relates to a methods for the isolation of nucleic acidscontained in particulate samples.

BACKGROUND OF INVENTION

The analysis of samples for microorganisms, such as bacteria, isimportant for public health. Foods grown, purchased, and consumed by thegeneral population may contain or acquire microorganisms, which flourishor grow as a function of the environment in which they are located. Thisgrowth may lead to accelerated spoilage of the food product or theproliferation of pathogenic organisms, which may produce toxins orallergens.

In current testing of foods for pathogens by PCR, the analytical methodmust be able to detect as little as one organism in 375 g of meat thatis incubating in four liters of enrichment broth. In order to bereliably assayed, the pathogen organisms must grow to a concentration ofapproximately 5,000 organisms per milliliter from which a fivemicroliter sample is collected for the PCR amplification and thedetection process. The time consumed for this growth ranges from eightto 24 or more hours. In order to reduce this time, a method is neededthat can concentrate the organisms from an incubating broth withoutintroducing the problems related to antibody-antigen interactions.

SUMMARY OF INVENTION

One aspect is for a process for collecting nucleic acids from aparticulate sample comprising:

-   -   (a) mixing an aliquot of a particulate sample containing nucleic        adds with a nucleic acid binding solution;    -   (b) exposing the mixture of step (a) to ultrasound;    -   (c) transferring the mixture of step (b) into a device        comprising a chamber interior comprising a fibrous nucleic acid        binding surface, the chamber interior being capable of expanding        in size in at least one dimension; the fibers of the fibrous        nucleic acid binding surface expanding to at least partially        fill the chamber interior upon wetting with the mixture;    -   (d) expelling the mixture from the device by compression of the        fibrous nucleic acid binding surface while retaining the fibrous        nucleic acid binding surface in the chamber interior;    -   (e) transferring an aliquot of elution buffer into the device;    -   (f) mixing the elution buffer with the fibrous nucleic acid        binding surface; and    -   (g) expelling the elution buffer from the device by compression        of the fibrous nucleic acid binding surface while retaining the        fibrous nucleic acid binding surface in the chamber interior,        whereby the elution buffer contains nucleic acids from the        particulate sample.

Another aspect is for a process for collecting nucleic acids from aparticulate sample comprising:

-   -   (a) transferring an aliquot of a particulate sample containing        nucleic acids into a device comprising        -   (i) a chamber interior comprising a fibrous nucleic acid            binding surface, the chamber interior being capable of            expanding in size in at least one dimension; and        -   (ii) a nucleic acid binding solution;        -   the fibers of the fibrous nucleic acid binding surface            expanding to at least partially fill the chamber interior            upon wetting with the particulate sample and the nucleic            acid binding solution;    -   (b) exposing the device and its contents to ultrasound;    -   (c) mixing the particulate sample with the nucleic acid binding        solution;    -   (d) expelling the nucleic acid binding solution from the device        by compression of the fibrous nucleic acid binding surface while        retaining the fibrous nucleic acid binding surface in the        chamber interior;    -   (e) transferring an aliquot of elution buffer into the device;    -   (f) mixing the elution buffer with the fibrous nucleic acid        binding surface; and    -   (g) expelling the elution buffer from the device by compression        of the fibrous nucleic acid binding surface while retaining the        fibrous nucleic acid binding surface in the chamber interior,        whereby the elution buffer contains nucleic acids from the        particulate sample.

A further aspect is for a process for collecting nucleic acids from aparticulate sample comprising:

-   -   (a) mixing an aliquot of a particulate sample containing nucleic        acids with a nucleic acid binding solution;    -   (b) exposing the mixture of step (a) to ultrasound;    -   (c) transferring the mixture of step (b) into a device        comprising a chamber interior comprising a fibrous nucleic acid        binding surface, the chamber interior being capable of expanding        in size in at least one dimension; the fibers of the fibrous        nucleic acid binding surface expanding to at least partially        fill the chamber interior upon wetting with the mixture;    -   (d) expelling the mixture from the device by compression of the        fibrous nucleic acid binding surface while retaining the fibrous        nucleic acid binding surface in the chamber interior;    -   (e) powderizing the fibrous nucleic acid binding surface;    -   (f) contacting an elution buffer with the powderized nucleic        acid binding surface; and    -   (g) separating the elution buffer from the powderized nucleic        acid binding surface, whereby the elution buffer contains        nucleic acids from the particulate sample.

An additional aspect is for a process for collecting nucleic acids froma particulate sample comprising:

-   -   (a) transferring an aliquot of a particulate sample containing        nucleic acids into a device comprising        -   (i) a chamber interior comprising a fibrous nucleic acid            binding surface, the chamber interior being capable of            expanding in size in at least one dimension; and        -   (ii) a nucleic acid binding solution;        -   the fibers of the fibrous nucleic acid binding surface            expanding to at least partially fill the chamber interior            upon wetting with the particulate sample and the nucleic            acid binding solution;    -   (b) exposing the device and its contents to ultrasound;    -   (c) mixing the particulate sample with the nucleic acid binding        solution;    -   (d) expelling the nucleic acid binding solution from the device        by compression of the fibrous nucleic acid binding surface while        retaining the fibrous nucleic acid binding surface in the        chamber interior;    -   (e) powderizing the fibrous nucleic acid binding surface;    -   (f) contacting an elution buffer with the powderized nucleic        acid binding surface; and    -   (g) separating the elution buffer from the powderized nucleic        acid binding surface, whereby the elution buffer contains        nucleic acids from the particulate sample.

Another aspect is for a process for collecting nucleic acids from aparticulate sample comprising:

-   -   (a) transferring an aliquot of a particulate sample containing        nucleic acids into a device comprising        -   (i) a chamber interior comprising a fibrous nucleic acid            binding surface, the chamber interior being capable of            expanding in size in at least one dimension; and        -   (ii) a nucleic acid binding solution;        -   the fibers of the fibrous nucleic acid binding surface            expanding to at least partially fill the chamber interior            upon wetting with the particulate sample and the nucleic            acid binding solution;    -   (b) mixing the particulate sample with the nucleic acid binding        solution;    -   (c) expelling the nucleic acid binding solution from the device        by compression of the fibrous nucleic acid binding surface while        retaining the fibrous nucleic acid binding surface in the        chamber interior;    -   (d) powderizing the fibrous nucleic acid binding surface;    -   (e) contacting an elution buffer with the powderized nucleic        acid binding surface; and    -   (f) separating the elution buffer from the powderized nucleic        acid binding surface, whereby the elution buffer contains        nucleic acids from the particulate sample.

An additional aspect is for a process for collecting nucleic acids froma particulate sample comprising:

-   -   (a) exposing an aliquot of a particulate sample containing        nucleic acids to a nucleic acid binding surface in the presence        of a nucleic acid binding solution, said nucleic acid binding        surface comprising a fibrous material capable of expansion upon        wetting;    -   (b) binding the nucleic acids to the nucleic acid binding        surface by expanding the fibrous material;    -   (c) separating the particulate sample from the nucleic acid        binding surface comprising nucleic acids bound thereto by        compression of the fibrous material;    -   (d) washing the nucleic acid binding surface with a wash        solution whereby the fibrous material is again expanded;    -   (e) separating the wash solution from the nucleic acid binding        surface comprising nucleic acids bound thereto by compression of        the fibrous material;    -   (f) powderizing the nucleic acid binding surface;    -   (g) exposing an aliquot of elution buffer to the nucleic acid        binding surface; and    -   (h) eluting nucleic acids from the nucleic acid binding surface.

Other objects and advantages will become apparent to those skilled inthe art upon reference to the detailed description that hereinafterfollows.

BRIEF DESCRIPTION OF THE FIGURES

General: BAX® system detection results are shown in many of thefollowing figures. In all cases, (+) signs are interpreted as a positivedetection response for the target organism, (−) signs are interpreted asa negative detection response, and (?) signals are interpreted assamples which encountered an error due to shutdown of the PCR reaction.In general, increased intensity of the red or blue target curves (alarger increase on the y-axis) is observed when the PCR reaction is morerobust. This occurs because of increased target organism concentration,decreased PCR inhibition, or both.

FIG. 1: BAX® PCR Signal Curves for unsonicated (Control) and samplessonicated with an ultrasonic horn for 30 sec. The sonicated sample showsincreased sensitivity, allowing 100 CFU/mL detection vs. control thatdoes not.

FIG. 2: E. coli O157:H7 detection results from RT BAX® in samples thatwere lightly sonicated in a water bath, and those aggressively sonicatedby an ultrasonic horn. Samples experiencing less ultrasonic energy didnot display detection beyond “B” level, which is 1000 CFU/mL, and showedsome PCR shutdown. Samples sonicated with an ultrasonic horn showdetection as low as “C/4” level, which is 25 CFU/mL, and do not displayPCR shutdown.

FIG. 3: BAX® Results from (a) control samples and (b) samples which weresonicated just prior to elution. No increase in process performance isobserved.

FIG. 4: Agarose gel picture and average recoveries showing crushingQuartzel® prior to elution resulted in DNA shearing and increasedelution efficiency.

FIG. 5: Crushing Quartzel® prior to elution allows detection of 100CFU/mL E. coli O157:H7 in ground beef enrichments with no PCR shutdown.

FIG. 6: All attempts to detect E. coli O157:H7 from ground beefutilizing a powdered silica capture substrate result in PCR shutdown.

FIG. 7: Combined ultrasonic treatment and substrate crushing allowsexcellent detection at 100 CFU/mL cell loading (24/24 attempts), andgood detection at 50 CFU/mL cell loading (5/6 attempts).

DETAILED DESCRIPTION OF PREFERRED EMBODIMENTS

Applicants specifically incorporate the entire contents of all citedreferences in this disclosure. Further, when an amount, concentration,or other value or parameter is given as either a range, preferred range,or a list of upper preferable values and lower preferable values, thisis to be understood as specifically disclosing all ranges formed fromany pair of any upper range limit or preferred value and any lower rangelimit or preferred value, regardless of whether ranges are separatelydisclosed. Where a range of numerical values is recited herein, unlessotherwise stated, the range is intended to include the endpointsthereof, and all integers and fractions within the range. It is notintended that the scope of the invention be limited to the specificvalues recited when defining a range.

Definitions

In this disclosure, a number of terms and abbreviations are used. Thefollowing definitions are provided.

As used herein, the term “about” or “approximately” means within 20%,preferably within 10%, and more preferably within 5% of a given value orrange.

The term “comprising” is intended to include embodiments encompassed bythe terms “consisting essentially of” and “consisting of”. Similarly,the term “consisting essentially of” is intended to include embodimentsencompassed by the term “consisting of”.

“Polymerase chain reaction” is abbreviated PCR.

A “chaotrope” is any chemical substance which disturbs the orderedstructure of liquid water. Chaotropes facilitate, e.g., unfolding,extension, dissociation of proteins, and the hydrogen boding of nucleicacids. Exemplary chaotropic salts include sodium iodide, sodiumperchlorate, guanidinium thiocyanate, guanidinium isothiocyanate, andguanidinium hydrochloride.

The term “isolated” refers to materials, such as nucleic acid moleculesand/or proteins, which are substantially free or otherwise removed fromcomponents that normally accompany or interact with the materials in anaturally occurring environment. Isolated polynucleotides may bepurified from a host cell in which they naturally occur. The term alsoembraces recombinant polynucleotides and chemically synthesizedpolynucleotides.

The terms “polynucleotide”, “polynucleotide sequence”, “nucleic acid”,“nucleic acid sequence”, and “nucleic acid fragment” are usedinterchangeably herein. These terms encompass nucleotide sequences andthe like. A polynucleotide may be a polymer of RNA or DNA that issingle- or double-stranded, that optionally contains synthetic,non-natural or altered nucleotide bases. A polynucleotide in the form ofa polymer of DNA may be comprised of one or more strands of cDNA,genomic DNA, synthetic DNA, or mixtures thereof.

The term “silica” as used herein denotes materials which are mainlybuilt up of silicon and oxygen. These materials comprise, for example,silica, silicon dioxide, silica gel, fumed silica gel, diatomaceousearth, celite, talc, quartz, crystalline quartz, amorphous quartz,glass, glass particles including all different shapes of thesematerials. Glass particles, for example, may comprise particles ofcrystalline silica, soda-lime glasses, borosilicate glasses, andfibrous, non-woven glass.

As used herein, “ultrasound” and “ultrasonic” generally refer toacoustic disturbances in a frequency range above about 20 kHz and whichextend upwards to over 2 MHz.

Collection Methods

One embodiment disclosed herein relates to the use of ultrasonic energyto simultaneously shear large nucleic acid molecules and largeparticulates to very small sizes prior to or during a chemical bindingstep to a capture substrate. Another embodiment involves crushing thecapture substrate prior to eluting the bound nucleic acid molecules toenable better wetting of the substrate and easier diffusion of boundnucleic acid molecules out of the substrate. The basic steps ofdisclosed herein are as follows.

-   -   1. To a container is added a particulate sample containing        nucleic acids and a nucleic acid binding solution. In some        embodiments, this solution is treated with ultrasonic energy and        exposed (simultaneously, afterward, or both) to a fibrous        nucleic acid binding surface. After mixing and brief exposure,        the solution is expelled leaving behind the nucleic acids bound        to the fibrous nucleic acid binding surface.    -   2. Optionally, wash the surface with solvents that remove        proteins, fats, and other impurities that remain.    -   3. In some embodiments, crush the nucleic acid binding surface        to generate a fine powder.    -   4. Release the nucleic acids with a buffer compatible with PCR        amplification and fluorescent detection using a volume of buffer        10 to 10,000 times smaller than the original sample volume.

The disclosed collection methods result in a concentration of nucleicacids 10 to 10,000 times higher than in the original sample and withoutthe presence of the PCR inhibitory components.

As noted above, in embodiments employing ultrasonic energy to shearlarge nucleic acids and reduce the size of particulates, the ultrasonicenergy can be employed simultaneous with or after exposure to a nucleicacid binding surface. Co-owned, co-pending PCT Application No.PCT/US2010/044083, discloses separation of nucleic acids fromparticulate samples using nucleic acid binding surface fibers. Asdiscussed therein, a particulate sample may be mixed with nucleic acidbinding surface fibers in a chamber, and when that chamber is compressedand its contents released through an orifice, the fibers remain in thechamber whereas the particles are expelled. If this process is performedin the presence of a chaotrope, the nucleic acid binding surface fibersexpand during mixing to infiltrate the bulk of the particulate sampleand collect a substantial portion of the nucleic acids. Also, afterexpulsion of liquids in the chamber, wash volumes may be introduced tothe fiber with the nucleic acid binding surface fibers again expandingto the volume. When these wash volumes are expelled, remainingparticulates are also expelled resulting in a small, compressed, mass ofnucleic acid binding surface fibers being a very small volume of theoriginal enrichment and presenting most of the target nucleic acids. Thenucleic acids may be released from the nucleic acid binding surfacefiber surface into a small volume of eluent producing a largeconcentration amplification of the target.

Ultrasound used in accordance with this invention consists of sound-likewaves whose frequency is above the range of normal human hearing, i.e.,above 20 kHz (20,000 cycles per second). Ultrasonic energy withfrequencies as high as 10 gigahertz (10,000,000,000 cycles per second)has been generated, but for the purposes of this invention, usefulresults will be achieved with frequencies within the range of from about20 kHz to about 2.5 Mhz, preferably of about 20 kHz to about 100 kHz.Ultrasonic waves can be generated from mechanical, electrical,electromagnetic, or thermal energy sources.

The intensity of the sonic energy may vary widely. For the purposes ofthis invention, best results will generally be achieved with anintensity ranging from about 1 W/cm² to about 30 W/cm². The typicalelectromagnetic source is a magnetostrictive transducer which convertsmagnetic energy into ultrasonic energy by applying a strong alternatingmagnetic field to certain metals, alloys and ferrites. The typicalelectrical source is a piezoelectric transducer, which uses natural orsynthetic single crystals (such as quartz) or ceramics (such as bariumtitanate or lead zirconate) and applies an alternating electricalvoltage across opposite faces of the crystal or ceramic to cause analternating expansion and contraction of crystal or ceramic at theimpressed frequency. The various methods of producing and applyingultrasonic energy, and commercial suppliers of ultrasound equipment, arewell known among those skilled in ultrasound technology.

The residence time of exposure of the particulate sample to ultrasoundis not critical to the practice or the success of the invention, and theoptimal residence time will vary according to the type of particulatesample being treated. Best results, however, will generally be obtainedwith residence times ranging from about 1 second to about 2 minutes,preferably about 1 second to about 30 seconds.

In one embodiment, an aliquot of a particulate sample containing nucleicacids is transferred into a device comprising a chamber interiorcomprising a fibrous nucleic acid binding surface, the chamber interiorbeing capable of expanding in size in at least one dimension; and anucleic acid binding solution; the fibers of the fibrous nucleic acidbinding surface expanding to at least partially fill the chamberinterior upon wetting with the particulate sample and the nucleic acidbinding solution. A typical sample enrichment protocol for diarrheagenicE. coli is described in the Bacteriological Analytical Manual, “BAM”(U.S. Food and Drug Administration): Aseptically weigh 25 g of sampleinto 225 ml of Brain Heart Infusion (BHI) broth (dilution factor of1:10). If necessary, sample size may deviate from 25 g depending onavailability of the sample, as long as the diluent is adjustedproportionally. Blend or stomach briefly. Incubate the homogenate for 10min at room temperature with periodic shaking then allow the sample tosettle by gravity for 10 min. Decant medium carefully into a sterilecontainer and incubate for 3 h at 35° C. to resuscitate injured cells.Transfer contents to 225 mL double strength Tryptone Phosphate (TP)broth in a sterile container and incubate 20 h at 44.0±0.2° C. It isnoted, however, that any sample enrichment procedure can be utilized inthe present processes.

Inside the chamber resides a fibrous nucleic acid-binding surface.Preferably, the fibrous nucleic acid-binding surface is non-magnetic. Insome embodiments this fibrous nucleic acid-binding surface is a cleansilica surface, with some embodiments utilizing a clean, activatedsilica surface. Cleaning and activation of the silica is effectuated,e.g., by washing with hydrochloric acid although a separate cleaningstep may not be required for all silica types. Following the cleaningstep the cleaning solution is expelled and the enriched particulatesample, e.g. a food sample, clinical sample, environmental sample, or aresearch sample, containing nucleic acids is aspirated.

Alternatively, the nucleic acid-binding surface can be, e.g., NOMEX®fibers (meta-aramid; E. I. du Pont de Nemours & Co., Wilmington, Del.),KEVLAR® (para-aramid; E. I. du Pont de Nemours & Co., Wilmington, Del.),a polyamide, e.g., nylon (e.g., nylon 6,6, nylon 6, nylon 11, nylon 12,nylon 612).

In embodiments utilizing ultrasound after exposure to a nucleic acidbinding surface, ultrasonic energy can be applied directly to thechamber containing the nucleic acid binding surface. In embodimentswhere the chamber is a plastic syringe or plastic vial, a one inchdiameter cylindrical horn can be used, with a tip that has been machinedto match the profile of the end of a syringe or vial. This is done toensure maximum contact between the horn and the syringe to maximize thetransfer of sound energy into the fluid (see co-owned, co-filed, U.S.Patent Application Ser. No. 61/452,683, incorporated herein byreference). If a vial is used, the horn tip can be machined to match theprofile of the end of the vial. To improve energy transfer, fluids suchas oils can be used to improve sound coupling.

An alternate embodiment uses an ultrasonic transducer, booster, horn,and anvil to clamp a liquid filled syringe or vial in a way thattransmits sound energy into the side of the syringe or vial. The horntip and mating anvil have a semi-cylindrical cut in their ends that istransverse to the horn and transducer axis and whose radius is matchedto the syringe or vial cylindrical radius. The diameter of the horn isadjusted to match the height of the liquid in the syringe or vial.

Preferably, ultrasonic energy is applied to the outside of the chamber,the sound thereby be conducted through the chamber wall, to avoid, forexample, cross-contamination when multiple samples are involved.Applying the ultrasonic energy to the outside of the chamber also hasthe advantage of avoiding the need to clean the ultrasound-generatingdevice between samples.

Typically, the volume of sample may range from 500 μL to 10 mL or higherdepending on sample type. An equal volume of nucleic acid bindingsolution containing, in some embodiments, detergent,ethylenediaminetetraacetic add (EDTA), buffering components and possiblyother components to facilitate binding and lysis is then aspirated withthe sample. The nucleic acid binding solution is typically a chaotropicsalt but alternatively can be a blend of salts such as 6 M NaClO₄, Tris,and trans-1,2-cyclohexanediaminetetraacetic acid (CDTA); or 8 M NaClO₄and Tris at pH 7.5; or NaI.

The solutions within the chamber are mixed thoroughly (on, for example,a vortex mixer) causing the fibrous nucleic acid-binding surface todisperse fully and expose the bulk of its surface area throughout theliquid in the chamber. The device is then incubated during which timecell lysis (if cells are present) and nucleic acid binding occurs. Anexemplary mixing condition is at room temperature for 15 minutes on arotating mixer.

After mixing, the nucleic acid binding solution is expelled from thedevice by compression of the fibrous nucleic acid binding surface whileretaining the fibrous nucleic acid binding surface in the chamberinterior.

As an example, using the chamber described above, an aliquot of a foodsample incubation broth containing microorganisms is pulled into thechamber of the device, and the broth is mixed with the nucleic acidbinding solution within the chamber. After mixing, the nucleic acidbinding solution is expelled from the chamber, but nucleic acids withinthe microorganisms bind to the fibrous nucleic acid-binding surface andare thereby retained within the chamber.

In some embodiments, the fibrous nucleic acid binding surface can thenbe washed with a wash solution. Following the initial sample incubationafter the liquid is expelled from the device, an equal volume of washbuffer containing the nucleic acid binding solution, detergent, andbuffering salts can be aspirated into the device. The device can then bemixed, e.g., on a vortex mixer as before, to expose fully the fibrousnucleic acid binding surface, and the wash fluid is then immediatelyexpelled, while retaining the fibrous nucleic acid binding surface inthe chamber interior.

Further, an equal volume of ethanol (e.g., 70% ethanol) can then beaspirated, mixed as before, and expelled. Next, an equal volume ofacetone can be aspirated, mixed as before, and expelled.

The wash solution is selected such that a release of the nucleic acidsfrom the fibrous nucleic acid binding surface preferably does not takeplace—or at least not in any significant amount—yet any impuritiespresent are washed out as well as possible. The contaminated washsolution is preferably removed in the same manner as the nucleic acidbinding solution at the end of the binding of the nucleic acids.

Any conventional wash buffer or any other suitable medium can be used aswash solution. Generally buffers with low or moderate ionic strength arepreferred such as, for example, 10 mM Tris-HCl at a pH of 8, 0-10 mMNaCl. In addition, however, wash buffers that have higher saltconcentrations—such as, for example, 3 M guanidinium hydrochloride—canalso be used. Equally, other standard media for carrying out the washingstep can be used, for example acetone or alcohol containing media suchas, for example, solutions of lower alkanols with one to five carbonatoms, preferably solutions of ethanol in water and especially preferredaqueous 70% ethanol. In another preferred embodiment, the wash solutionis isopropanol.

In some embodiments, the washing solution is characterized in that thenucleic acid binding solution, particularly a chaotropic substance, isnot contained therein. As a result, a possibility of having thechaotropic substance incorporated into a recovery step after the washingstep can be reduced. In the elution step, where the chaotropic substanceis incorporated thereinto, the chaotropic substance sometimes hinders alater enzyme reaction such as PCR reaction or the like; thereforeconsidering the later enzyme reaction, not including the chaotropicsubstance to a washing solution is preferable.

Following expulsion of the nucleic acid binding solution from thechamber, or following the optional wash step(s) if utilized, the fibrousnucleic acid binding surface can be dried by placing the device in,e.g., a heat block (e.g., at 55° C. for 15 minutes). In anotherembodiment, the optional drying step can be performed by use of avacuum.

After the optional washing and/or drying steps, the fibrous nucleic acidbinding surface can be powderized to enable better wetting of thenucleic acid binding surface and easier diffusion of bound nucleic acidmolecules out of the nucleic acid binding surface. The powderizationstep produces a plurality of fine powders. Preferably, the averageparticle long axis length will be reduced to below about 20 μm. It ispossible to powderize the nucleic acid bind surface by employing aconventionally publicly-known method such as crushing, grinding,shearing, pulverizing, cutting, shredding, hammering, sanding, milling,or a combination thereof. In a preferred embodiment, the nucleic acidbinding surface is crushed into a powder by placing the nucleic acidbinding surface into a chamber (e.g., a spin column) and pulverizing thenucleic acid binding surface with a pestle-like device (in the case of aspin column, a syringe plunger with a sharp surface can be used).

The captured nucleic acid is eluted by exposure to a small volume (e.g.,70-100 μl) of an elution buffer. A typical elution buffer is a PCRbuffer solution pH 8.3 containing all the necessary components for PCR(i.e., MgCl₂, buffering salts, etc.) but not containing a chaotropicsalt. The selection of the elution buffer is determined in part by thecontemplated use of the isolated nucleic acids. Examples of suitableelution buffers are TE buffer, aqua bidest and PCR buffer. It ispreferred that pH of a elution solution is 2 to 11 and, more preferably,5 to 9. In addition, ionic strength and salt concentration particularlyaffect the elution of adsorbed nucleic acid. Preferably, the elutionsolution has an ionic strength of 290 mmol/L or less and has a saltconcentration of 90 mmol/L or less. As a result thereof, recovering rateof nucleic acid increases and much more nucleic acid is able to berecovered.

When mixing is complete, the elution buffer is expelled from the device,with the elution buffer containing nucleic acids that previous werebound to the nucleic acid-binding surface. As necessary, additionalelution buffer can be pulled into the device, mixed with the nucleicacid-binding surface, and expelled from the device to maximize recoveryof bound nucleic acids. Because the solution resulting from the contactwith the nucleic acid-binding surface contains the adsorbed nucleicacids, the recovered solution is typically subjected to a followingstep, for example PCR amplification of the nucleic acids.

Also, in the elution step, it is possible to add a stabilizing agent forpreventing degradation of nucleic acid recovered in the elution solutionof nucleic acid. As the stabilizing agent, an antibacterial agent, afungicide, a nucleic acid degradation inhibitor and the like can beadded. As the nuclease inhibitor, EDTA and the like can be cited.

There is no limitation for the infusing times for a elution buffer andthat may be either once or plural times. Usually, when nucleic acid isto be separated and purified quickly and simply, that is carried out bymeans of one recovery while, when a large amount of nucleic acid is tobe recovered, elution buffer may be infused for several times.

By way of the above methods, nucleic acids can be recovered from amyriad of microorganisms including, e.g., bacteria, fungi, algae, orviruses.

EXAMPLES

The present invention is further defined in the following Examples. Itshould be understood that these Examples, while indicating preferredembodiments of the invention, are given by way of illustration only.

The meaning of abbreviations is as follows: “h” means hour(s), “min”means minute(s), “sec” means second(s), “d” means day(s), “mL” meansmilliliter(s), “μL” means microliter(s), “CFU” means colony formingunit(s), “MP” means multiplex, “BHI” means brain heart infusion, “BPW”means buffered peptone water, “n.d.” means no data, “EDTA” meansethylenediaminetetraacetic acid.

Example 1

25 g of ground beef was stomached for 30 sec and enriched in 225 mL ofMP media (BAX® System MP Media for E. coli O157:H7, DuPont Qualicon,Wilmington, Del.) overnight. Various aliquots of this enrichment werespiked with several concentrations of E. coli O157:H7. 2 mL of theground beef enrichment was mixed with 1 mL of a chaotropic bindingbuffer solution (5.2 M guanidinium thiocyanate, 22 mM EDTA, 1.3% byweight Triton X-100 in 50 mM Tris-Cl pH 6.4) in a 15 mL falcon tube andsonicated for 30 sec with either an ultrasonic water bath (relativelylow energy sonication) or an ultrasonic horn (relatively high energysonication) or not at all (controls). The sonicated solution was addedto a 5 mL polypropylene syringe which contained 10 mg of Quartzel® wool(4 μm fiber size (Saint-Gobain Quartz, Northboro, Mass.)). The samplewas left in contact with the Quartzel® wool for five minutes, and wasejected from the syringe manually. Next, 3 mL of isopropanol was addedto the syringe (which still contains the Quartzel® wool). Theisopropanol wash was held in the syringe for 1 minute, and finallyremoved from the syringe via a vacuum manifold. Active vacuum was pulledon the syringe (with plunger removed) for 5 minutes to ensure that theQuartzel® wool was dry. 100 μL of BAX® lysis buffer was added to theQuartz wool and allowed to sit for 5 minutes. The buffer was finallyejected from the syringe by depressing a clean plunger into the syringe.This solution was used for standard RT BAX® PCR-based detection of E.coli O157:H7.

Ultrasonic treatment of food enrichment samples prior to DNA extractionand concentration shows a dramatic improvement in PCR signal (FIGS. 1and 2) and Inhibition (FIG. 2).

Comparative Example 1

25 g of ground beef was stomached for 30 sec and enriched in 225 mL ofMP media overnight. Various aliquots of this enrichment were spiked withseveral concentrations of E. coli O157:H7. 2 mL of the ground beefenrichment was mixed with 1 mL of a chaotropic binding buffer solutionin a 3 mL polypropylene syringe which contained 10 mg of Quartzel® wool(4 μm fiber size). The sample was left in contact with the Quartzel®wool for five minutes, and was ejected from the syringe manually. Next,3 mL of isopropanol was added to the syringe (which still contains theQuartzel® wool). The isopropanol wash was held in the syringe for 1minute, and finally removed from the syringe via a vacuum manifold.Active vacuum was pulled on the syringe (with plunger removed) for 5minutes to ensure that the Quartzel® wool was dry. 100 μL of BAX® lysisbuffer was added to the Quartz wool—some samples were sonicated byexternal syringe contact with an ultrasonic horn while controls werenot. All samples were allowed to sit for 5 minutes. The buffer wasfinally ejected from the syringe by depressing a clean plunger into thesyringe. This solution was used for standard RT BAX® PCR-based detectionof E. coli O157:H7.

Sonication of sample just prior to elution does not improve efficiency(FIG. 3).

Example 2

For each sample, 1 mL E. coli DNA (5 ng/μl, Type VIII, 15-113 kbp,Sigma) was mixed with 1 mL L6 Buffer and added into the syringesdevices. Each syringe device contained ten 1 mg pieces of 4 μm Quartzel®fiber. Devices were capped, inverted eight times to mix, and sat for 5min at room temperature. The caps were removed and samples were allowedto drain by passive flow. Fibers were washed with 3 mL of isopropanoland dried by vacuum for 5 min. Each fiber was then transferred into aPierce Handee microfuge column (#89868, Thermo Scientific, Rockford,Ill.) containing a 30 μm pore size filter that would retain the fiberafter centrifugation. For three of the six the samples, fibers wereground into a powder using a pipet tip. One hundred twenty microlitersof 10 mM Tris-Cl pH 8.5 were added to each fiber and samples sat for 5min at room temperature to elute the DNA. The columns were thencentrifuged for 30 sec at 10000 rpm to collect the eluate. Another 120μL elution buffer was added and samples sat again for 5 min. Sampleswere then spun and the eluted DNA was collected into fresh tubes. Twentymicroliters of the samples were run on a 1% agarose gel stained withethidium bromide. The DNA yield was also quantified by optical density(OD260) and expressed as percent recovery.

Results are shown in FIG. 4. The pulverized fiber/DNA resulted in theexpected DNA shearing and also in higher DNA recovery with the firstelution.

Example 3

25 g of ground beef was stomached for 30 sec and enriched in 225 mL ofMP media overnight. Various aliquots of this enrichment were spiked withseveral concentrations of E. coli O157:H7. 2 mL of the ground beefenrichment was mixed with 1 mL of a chaotropic binding buffer solutionand added to a 5 mL polypropylene syringe which contained 10 mg ofQuartzel® wool (4 μm fiber size). The sample was left in contact withthe Quartzel® wool for five minutes, and was ejected from the syringemanually. Next, 3 mL of isopropanol was added to the syringe (whichstill contains the Quartzel® wool). The isopropanol wash was held in thesyringe for 1 minute, and finally removed from the syringe via a vacuummanifold. Active vacuum was pulled on the syringe (with plunger removed)for 5 minutes to ensure that the Quartzel® wool was dry. Next, theQuartzel® wool was moved into a Qiagen DNEasy spin column and crushedand pulverized with a syringe plunger that had been scratched with ablade (so that it was rough and sharp). The crushing procedure involvedsqueezing the wool in the column and turning the plunger 10×. The woolwould become like a powder during this process. 100 μL of BAX® lysisbuffer was added to the Quartz wool and allowed to sit for 5 minutes.The buffer was finally ejected from the syringe by depressing a cleanplunger into the syringe. This solution was used for standard RT BAX®PCR-based detection of E. coli O157:H7.

Crushing fiber prior to elution allows 100 CFU/mL detection of E. coliO157:H7 in ground beef (FIG. 5).

Comparative Example 2

25 g of ground beef was stomached for 30 sec and enriched in 225 mL ofMP media overnight. Various aliquots of this enrichment were spiked withseveral concentrations of E. coli O157:H7. 2 mL of the ground beefenrichment was mixed with 1 mL of a chaotropic binding buffer solutionin a 3 mL microcentrifuge tube containing 10 mg of vitreous silica(Sigma, 0.5-10 μm particle diameter). The tube was vortexed and held for5 minutes, then spun down at 10000 rpm for 30 sec to pellet the silica.The supernatant was removed, and an attempt was made to resuspend thepellet in 3 mL isopropanol via vortexing. The pellet would not resuspendwell, and was spun down again at 10000 rpm for 30 sec. The isopropanolwas decanted off, and the pellet again washed with isopropanol by thesame procedure. Next, the silica powder was dried in a heat block at 80°C. for 30 minutes to ensure removal of all isopropanol. Finally, thesilica was exposed to 100 μL of BAX® lysis buffer, vortexed for 30 sec,and incubated at room temp for 5 minutes. The silica was spun down onefinal time at 10000 rpm for 30 sec, and 30 μL of the solution wasdecanted from above the silica pellet and used in standard E. colireal-time BAX® protocols.

The results are shown in FIG. 6, which show major issues with PCRshutdown.

Example 4

25 g of ground beef was stomached for 30 sec and enriched in 225 mL ofMP media for 6 h. Various aliquots of this enrichment were spiked withseveral concentrations of E. coli O157:H7. 2 mL of the ground beefenrichment was mixed with 1 mL of a chaotropic binding buffer solutionin a 5 mL PP tube and sonicated for 30 sec with an ultrasonic horn(relatively high energy sonication). The sonicated solution was added toa 5 mL polypropylene syringe which contained 10 mg of Quartzel® wool (4μm fiber size). The sample was left in contact with the Quartzel® woolfor five minutes, and was ejected from the syringe manually. Next, 3 mLof isopropanol was added to the syringe (which still contains theQuartzel® wool). The isopropanol wash was held in the syringe for 1minute, and finally removed from the syringe via a vacuum manifold.Active vacuum was pulled on the syringe (with plunger removed) for 5minutes to ensure that the Quartzel® wool was dry. Next, the Quartzel®wool was moved into a Qiagen DNEasy spin column and crushed andpulverized with a syringe plunger that had been scratched with a blade(so that it was rough and sharp). The crushing procedure involvedsqueezing the wool in the column and turning the plunger 10×. The woolwould become like a powder during this process. 100 μL of BAX® lysisbuffer was added to the Quartz wool and allowed to sit for 5 minutes.The buffer was finally ejected from the syringe by centrifugation at10000 rpm for 30 sec. This solution was used for standard RT BAX®PCR-based detection of E. coli O157:H7.

Samples prepared utilizing ultrasonic treatment and substrate crushingdemonstrate excellent detection capability (FIG. 7).

What is claimed is:
 1. A process for collecting nucleic acids from aparticulate sample comprising: (a) mixing an aliquot of a particulatesample containing nucleic acids with a nucleic acid binding solution;(b) shearing the nucleic acids in the mixture of step (a) by ultrasound;(c) transferring the mixture of step (b) into a device comprising achamber interior comprising a fibrous nucleic acid binding surface, thechamber interior being capable of expanding in size in at least onedimension; the fibers of the fibrous nucleic acid binding surfaceexpanding to at least partially fill the chamber interior upon wettingwith the mixture; (d) expelling the mixture from the device bycompression of the fibrous nucleic acid binding surface while retainingthe fibrous nucleic acid binding surface in the chamber interior; (e)powderizing the fibrous nucleic acid binding surface; (f) contacting thepowderized nucleic acid binding surface with an elution buffer; and (g)separating the elution buffer from the powderized nucleic acid bindingsurface, whereby the elution buffer contains nucleic acids from theparticulate sample.
 2. The process of claim 1 comprising after step (d)and before step (e) the further steps of: washing the fibrous nucleicacid binding surface with a wash solution; and expelling the washsolution by compression of the fibrous nucleic acid binding surfacewhile retaining the fibrous nucleic acid binding surface in the chamberinterior.
 3. The process of claim 2, wherein the expelling is performedby vacuum.
 4. The process of claim 1, wherein the expelling of step (d)is performed by vacuum.
 5. The process of claim 1, wherein the fibrousnucleic acid binding surface is non-magnetic.
 6. The process of any ofclaims 1-5, wherein the fibrous nucleic acid binding surface is a cleansilica surface.
 7. The process of claim 6, wherein the clean silicasurface is a clean, activated silica surface.
 8. The process of claim 7,wherein the clean, activated silica surface comprises silica wool. 9.The process of any of claims 1-5, wherein the nucleic acid bindingsolution comprises a chaotropic salt.
 10. The process of any of claims1-5, wherein the particulate sample comprises eukaryotic cells,prokaryotic cells, viruses, and a combination thereof.
 11. The processof any of claims 1-5, wherein the particulate sample is a food sample ora clinical sample.
 12. A process for collecting nucleic acids from aparticulate sample comprising: (a) transferring an aliquot of aparticulate sample containing nucleic acids into a device comprising (i)a chamber interior comprising a non-magnetic fibrous nucleic acidbinding surface, the chamber interior being capable of expanding in sizein at least one dimension; and (ii) a nucleic acid binding solution; thefibers of the non-magnetic fibrous nucleic acid binding surfaceexpanding to at least partially fill the chamber interior upon wettingwith the particulate sample and the nucleic acid binding solution; (b)shearing the nucleic acids in the sample by ultrasound; (c) mixing theparticulate sample with the nucleic acid binding solution; (d) expellingthe nucleic acid binding solution from the device by compression of thenon-magnetic fibrous nucleic acid binding surface while retaining thenon-magnetic fibrous nucleic acid binding surface in the chamberinterior; (e) removing the non-magnetic fibrous nucleic acid bindingsurface from the device; (f) powderizing the non-magnetic fibrousnucleic acid binding surface (g) contacting the powderized nucleic acidbinding surface with an elution buffer; and (h) separating the elutionbuffer from the powderized non-magnetic nucleic acid binding surface,whereby the elution buffer contains nucleic acids from the particulatesample.
 13. A process for collecting nucleic acids from a particulatesample comprising: (a) mixing an aliquot of a particulate samplecontaining nucleic acids with a nucleic acid binding solution; (b)shearing the nucleic acids in the mixture of step (a) by ultrasound; (c)transferring the mixture of step (b) into a device comprising a chamberinterior comprising a fibrous nucleic acid binding surface, the chamberinterior being capable of expanding in size in at least one dimension;the fibers of the fibrous nucleic acid binding surface expanding to atleast partially fill the chamber interior upon wetting with the mixture;(d) expelling the mixture from the device by compression of the fibrousnucleic acid binding surface while retaining the fibrous nucleic acidbinding surface in the chamber interior; (e) powderizing the fibrousnucleic acid binding surface; (f) contacting the powderized nucleic acidbinding surface with an elution buffer; and (g) separating the elutionbuffer from the powderized nucleic acid binding surface, whereby theelution buffer contains nucleic acids from the particulate sample. 14.The process of claim 13, wherein the fibrous nucleic acid bindingsurface is non-magnetic.
 15. The process of claim 13 comprising afterstep (d) and before step (e) the further step of removing the fibrousnucleic acid binding surface from the device.
 16. A process forcollecting nucleic acids from a particulate sample comprising: (a)transferring an aliquot of a particulate sample containing nucleic acidsinto a device comprising (i) a chamber interior comprising a fibrousnucleic acid binding surface, the chamber interior being capable ofexpanding in size in at least one dimension; and (ii) a nucleic acidbinding solution; the fibers of the fibrous nucleic acid binding surfaceexpanding to at least partially fill the chamber interior upon wettingwith the particulate sample and the nucleic acid binding solution; (b)shearing the nucleic acids in the sample by ultrasound; (c) mixing theparticulate sample with the nucleic acid binding solution; (d) expellingthe nucleic acid binding solution from the device by compression of thefibrous nucleic acid binding surface while retaining the fibrous nucleicacid binding surface in the chamber interior; (e) powderizing thefibrous nucleic acid binding surface; (f) contacting the powderizednucleic acid binding surface with an elution buffer; and (g) separatingthe elution buffer from the powderized nucleic acid binding surface,whereby the elution buffer contains nucleic acids from the particulatesample.
 17. The process of claim 16, wherein the fibrous nucleic acidbinding surface is non-magnetic.
 18. The process of claim 16 comprisingafter step (d) and before step (e) the further step of removing thefibrous nucleic acid binding surface from the device.
 19. The process ofclaim 1 comprising after step (d) and before step (e) the further stepsof: washing the fibrous nucleic acid binding surface with a washsolution; expelling the wash solution by compression of the fibrousnucleic acid binding surface while retaining the fibrous nucleic acidbinding surface in the chamber interior; and removing the fibrousnucleic acid binding surface from the device.